The 32-year-old centre-back will be sidelined for at least six months after scans confirmed he needs surgery.
Bosschaart, 32, will have an operation next month to repair a heel injury and a small tear in his Achilles tendon.
The 32-year-old former Feyenoord defender has been plagued by injuries in his two seasons at Sydney, suffering a separate Achilles tear at the end of the 2011/12 season which sidelined him for almost seven months.
He made his long-awaited comeback in the Sky Blues' 3-2 loss to Melbourne Victory in November, where he scored his first and only goal for Sydney, but played just six matches before being forced out by his current complaint.
"Got the results. ....news have a crack in my heel bone and tear in my achilles attachment. Which means i need an operation on the 4 of feb," Bosschaart tweeted.
"And gonna hold me on the sidelines for at least 6 months again. So a sad day for me. I will getting back harder and stronger."
The Sky Blues posted a dramatic last-minute 2-1 win over Melbourne Heart on Sunday to move off the bottom of the ladder into ninth spot.
But with the worst defence in the A-League - conceding 33 goals in the 16 rounds so far - they can ill afford to lose a solid centre-back the likes of Bosschaart.
Because of injuries coach Frank Farina has been forced to try 16-year-old Aaron Calver and also play utility Rhyan Grant in defence alongside the inexperienced Trent McClenahan to cover for the loss of regular defenders Bosschaart, Fabio and Adam Griffiths.
"It's definitely a blow for us but we will push on with the players who have been getting the job done in recent weeks," said Farina.
"Pascal is an experienced player and we will miss that experience as we move towards the business end of the season.
"It is a shame he picked up the injury as he was looking good after such a long lay off from the injury he suffered last year."